1 Loading data

Load the results of clinical information from TCGA pan cancer study.

## [1] 11160    34
## # A tibble: 2 x 34
##   ...1  bcr_patient_bar… type  age_at_initial_… gender race  ajcc_pathologic…
##   <chr> <chr>            <chr>            <dbl> <chr>  <chr> <chr>           
## 1 1     TCGA-OR-A5J1     ACC                 58 MALE   WHITE Stage II        
## 2 2     TCGA-OR-A5J2     ACC                 44 FEMALE WHITE Stage IV        
## # … with 27 more variables: clinical_stage <chr>, histological_type <chr>,
## #   histological_grade <chr>, initial_pathologic_dx_year <dbl>,
## #   menopause_status <chr>, birth_days_to <dbl>, vital_status <chr>,
## #   tumor_status <chr>, last_contact_days_to <dbl>, death_days_to <dbl>,
## #   cause_of_death <chr>, new_tumor_event_type <chr>,
## #   new_tumor_event_site <chr>, new_tumor_event_site_other <chr>,
## #   new_tumor_event_dx_days_to <dbl>, treatment_outcome_first_course <chr>,
## #   margin_status <chr>, residual_tumor <lgl>, OS <dbl>, OS.time <dbl>,
## #   DSS <dbl>, DSS.time <dbl>, DFI <dbl>, DFI.time <dbl>, PFI <dbl>,
## #   PFI.time <dbl>, Redaction <chr>
## 
## COAD LUAD LUSC SKCM 
##  459  522  504  470

Load the results of cell type fraction, and then merage them with clinical information. Save the information for each cancer type into a list named ctf (cell type fractions).

## 
## --------------------------------------------------------------
## COAD
## --------------------------------------------------------------
## 
## cell type fraction estimates from expression
## [1] 185   7
##            CD4T       CD8T   Monocyte          B         NK Neutrophil
## 5656 0.07627453 0.01670232 0.02561258 0.04381193 0.01982880 0.00652889
## 6781 0.06005796 0.12891577 0.10364729 0.07942259 0.05740941 0.04947972
##            Treg
## 5656 0.01124095
## 6781 0.02106727
## 
## cell type fraction estimates from methylation
## [1] 185   7   5
##                  EMeth          svr         ls         rls            qp
## CD4T       0.026415214 0.0319012555 0.00000000 0.000000000  2.000000e-01
## CD8T       0.003385372 0.0409917716 0.12346010 0.119316714 -8.686388e-18
## Monocyte   0.049698012 0.0576861975 0.03145094 0.032486828  1.205043e-16
## B          0.024464355 0.0532250575 0.02314771 0.024156154  0.000000e+00
## NK         0.010294409 0.0123506692 0.00000000 0.001562089  1.524040e-16
## Neutrophil 0.012566427 0.0029683220 0.02194124 0.022478216 -1.019300e-16
## Treg       0.073176210 0.0008767268 0.00000000 0.000000000 -3.707308e-17
## 
## --------------------------------------------------------------
## LUAD
## --------------------------------------------------------------
## 
## cell type fraction estimates from expression
## [1] 386   7
##           CD4T       CD8T   Monocyte         B         NK  Neutrophil Treg
## 2666 0.2116564 0.02985346 0.04384860 0.1298613 0.02478026 0.000000000    0
## 3918 0.2976973 0.00000000 0.08549598 0.1191329 0.03891238 0.008761388    0
## 
## cell type fraction estimates from methylation
## [1] 386   7   5
##                 EMeth         svr         ls        rls           qp
## CD4T       0.04277126 0.051700419 0.00000000 0.00000000 4.400000e-01
## CD8T       0.07050939 0.162606264 0.26055267 0.27921028 1.291454e-16
## Monocyte   0.03198820 0.060022761 0.04819152 0.03858709 2.720060e-17
## B          0.07414185 0.095191019 0.05165730 0.05069063 0.000000e+00
## NK         0.03264954 0.009494585 0.00000000 0.00000000 1.012392e-18
## Neutrophil 0.07449514 0.060984952 0.07959851 0.07151200 2.542433e-17
## Treg       0.11344463 0.000000000 0.00000000 0.00000000 4.502091e-18
## 
## --------------------------------------------------------------
## LUSC
## --------------------------------------------------------------
## 
## cell type fraction estimates from expression
## [1] 296   7
##           CD4T       CD8T   Monocyte          B         NK  Neutrophil
## 6546 0.1785366 0.07040708 0.08526741 0.21031966 0.03650193 0.001964585
## A50Z 0.1267777 0.00000000 0.06197406 0.06561747 0.09088046 0.276548787
##             Treg
## 6546 0.007002724
## A50Z 0.018201514
## 
## cell type fraction estimates from methylation
## [1] 296   7   5
##                    EMeth         svr          ls         rls           qp
## CD4T       -2.297196e-17 0.164670429 0.000000000 0.008166193 3.877593e-01
## CD8T        1.135327e-01 0.082647787 0.294630259 0.301378010 3.105060e-02
## Monocyte    1.492672e-01 0.156557168 0.155026869 0.150076818 1.233630e-02
## B           1.574076e-01 0.133672318 0.132459221 0.128402044 1.588538e-01
## NK          1.006683e-01 0.050492578 0.004148921 0.000000000 9.969011e-20
## Neutrophil  6.912424e-02 0.000000000 0.002147771 0.001976935 3.187354e-17
## Treg        0.000000e+00 0.001959721 0.001586959 0.000000000 0.000000e+00
## 
## --------------------------------------------------------------
## SKCM
## --------------------------------------------------------------
## 
## cell type fraction estimates from expression
## [1] 391   7
##           CD4T       CD8T   Monocyte           B         NK Neutrophil
## A51H 0.2188935 0.03499094 0.05367095 0.545323628 0.03791312 0.00000000
## A728 0.1688186 0.24422901 0.09891862 0.009328079 0.03907109 0.07365859
##             Treg
## A51H 0.009207837
## A728 0.075976001
## 
## cell type fraction estimates from methylation
## [1] 391   7   5
##                    EMeth         svr         ls         rls           qp
## CD4T        4.643562e-01 0.384154045 0.35310646 0.364675454 4.895262e-01
## CD8T       -1.163978e-17 0.000000000 0.00000000 0.000000000 5.345828e-19
## Monocyte   -5.503769e-19 0.033600316 0.04366372 0.035335965 2.338829e-18
## B           4.356438e-01 0.366820183 0.38580363 0.396619361 4.104738e-01
## NK         -1.734480e-19 0.009108515 0.01178413 0.001574085 1.531097e-17
## Neutrophil -4.341269e-18 0.000000000 0.00000000 0.000000000 3.956396e-20
## Treg       -1.391424e-18 0.106316941 0.10564205 0.101795135 0.000000e+00

2 Asess the association between cell type fractions and survival time

2.1 Association with each cell type

This function cox_summary summarizes the association between cell type composition and survival time.

Check the associations between cell type fractions and disease-specific survival.

## 
## --------------------------------------------------------------
## COAD
## --------------------------------------------------------------
##                  beta         HR (95% CI for HR) p.value
## CD4T.E         0.0225  1.02 (5.66e-01--1.85e+00)    0.94
## CD8T.E        -0.0135 0.987 (6.65e-01--1.46e+00)    0.95
## Monocyte.E    -0.0214 0.979 (6.00e-01--1.60e+00)    0.93
## B.E              0.15  1.16 (6.76e-01--2.00e+00)    0.59
## NK.E           -0.204 0.815 (5.18e-01--1.28e+00)    0.38
## Neutrophil.E   0.0544  1.06 (7.25e-01--1.54e+00)    0.78
## Treg.E       -0.00836 0.992 (6.42e-01--1.53e+00)    0.97
## CD4T          -0.0674 0.935 (6.89e-01--1.27e+00)    0.67
## CD8T           0.0362  1.04 (8.10e-01--1.33e+00)    0.77
## Monocyte       -0.129 0.879 (6.28e-01--1.23e+00)    0.45
## B              0.0833  1.09 (7.85e-01--1.50e+00)    0.62
## NK              -0.13 0.878 (6.16e-01--1.25e+00)    0.47
## Neutrophil    -0.0213 0.979 (7.32e-01--1.31e+00)    0.89
## Treg           0.0574  1.06 (7.79e-01--1.44e+00)    0.71
## 
## --------------------------------------------------------------
## LUAD
## --------------------------------------------------------------
##                  beta         HR (95% CI for HR) p.value
## CD4T.E         0.0165  1.02 (7.58e-01--1.36e+00)    0.91
## CD8T.E         0.0442  1.05 (8.82e-01--1.24e+00)    0.61
## Monocyte.E     0.0425  1.04 (8.12e-01--1.34e+00)    0.74
## B.E            -0.173 0.841 (6.71e-01--1.05e+00)    0.13
## NK.E            0.162  1.18 (9.13e-01--1.51e+00)    0.21
## Neutrophil.E   0.0571  1.06 (8.50e-01--1.32e+00)    0.61
## Treg.E         -0.122 0.885 (7.19e-01--1.09e+00)    0.25
## CD4T          -0.0412  0.96 (8.56e-01--1.08e+00)    0.48
## CD8T          -0.0285 0.972 (8.89e-01--1.06e+00)    0.53
## Monocyte      -0.0412  0.96 (7.98e-01--1.15e+00)    0.66
## B              -0.101 0.904 (7.85e-01--1.04e+00)    0.16
## NK              0.149  1.16 (9.75e-01--1.38e+00)   0.095
## Neutrophil   -0.00564 0.994 (8.69e-01--1.14e+00)    0.93
## Treg          0.00366     1 (8.98e-01--1.12e+00)    0.95
## 
## --------------------------------------------------------------
## LUSC
## --------------------------------------------------------------
##                 beta         HR (95% CI for HR) p.value
## CD4T.E        -0.198  0.82 (6.29e-01--1.07e+00)    0.15
## CD8T.E       -0.0374 0.963 (7.94e-01--1.17e+00)     0.7
## Monocyte.E    -0.126 0.881 (6.62e-01--1.17e+00)    0.39
## B.E           -0.124 0.883 (7.13e-01--1.09e+00)    0.25
## NK.E          -0.208 0.813 (6.14e-01--1.07e+00)    0.15
## Neutrophil.E  0.0935   1.1 (8.74e-01--1.38e+00)    0.42
## Treg.E        -0.114 0.892 (6.62e-01--1.20e+00)    0.45
## CD4T          0.0367  1.04 (9.06e-01--1.19e+00)     0.6
## CD8T         -0.0222 0.978 (8.75e-01--1.09e+00)     0.7
## Monocyte      0.0116  1.01 (8.47e-01--1.21e+00)     0.9
## B             -0.181 0.834 (7.22e-01--9.64e-01)   0.014
## NK           -0.0642 0.938 (7.84e-01--1.12e+00)    0.48
## Neutrophil   -0.0382 0.963 (8.36e-01--1.11e+00)    0.59
## Treg          0.0591  1.06 (9.32e-01--1.21e+00)    0.37
## 
## --------------------------------------------------------------
## SKCM
## --------------------------------------------------------------
##                 beta         HR (95% CI for HR) p.value
## CD4T.E        -0.163  0.85 (7.65e-01--9.44e-01)  0.0024
## CD8T.E        -0.145 0.865 (7.95e-01--9.40e-01) 0.00068
## Monocyte.E   -0.0737 0.929 (8.22e-01--1.05e+00)    0.24
## B.E           -0.103 0.902 (8.22e-01--9.90e-01)   0.029
## NK.E          -0.154 0.857 (7.53e-01--9.76e-01)    0.02
## Neutrophil.E  0.0205  1.02 (8.37e-01--1.24e+00)    0.84
## Treg.E        -0.133 0.875 (7.76e-01--9.87e-01)    0.03
## CD4T         -0.0164 0.984 (9.09e-01--1.06e+00)    0.68
## CD8T           -0.13 0.878 (8.21e-01--9.39e-01) 0.00015
## Monocyte     -0.0343 0.966 (8.90e-01--1.05e+00)    0.41
## B             -0.143 0.867 (7.95e-01--9.45e-01)  0.0011
## NK           -0.0887 0.915 (8.19e-01--1.02e+00)    0.12
## Neutrophil     0.113  1.12 (1.02e+00--1.23e+00)   0.015
## Treg           0.116  1.12 (1.03e+00--1.23e+00)   0.013

2.2 Association with relative cell type fractions

Check the associations between disease-specific survival and relative cell type fractions with respect to CD8 T cells.

## 
## --------------------------------------------------------------
## COAD
## --------------------------------------------------------------
##                     beta         HR (95% CI for HR) p.value
## CD4T.E_lr         0.0275  1.03 (6.70e-01--1.58e+00)     0.9
## Monocyte.E_lr   -0.00068 0.999 (5.41e-01--1.85e+00)       1
## B.E_lr             0.211  1.24 (6.74e-01--2.26e+00)    0.49
## NK.E_lr           -0.219 0.803 (4.90e-01--1.32e+00)    0.38
## Neutrophil.E_lr   0.0573  1.06 (7.45e-01--1.51e+00)    0.75
## Treg.E_lr        0.00902  1.01 (6.37e-01--1.60e+00)    0.97
## CD4T_lr           -0.104 0.901 (6.77e-01--1.20e+00)    0.47
## Monocyte_lr       -0.128  0.88 (6.62e-01--1.17e+00)    0.38
## B_lr              0.0318  1.03 (7.17e-01--1.49e+00)    0.86
## NK_lr            -0.0851 0.918 (7.28e-01--1.16e+00)    0.47
## Neutrophil_lr    -0.0285 0.972 (8.09e-01--1.17e+00)    0.76
## Treg_lr          0.00136     1 (8.19e-01--1.22e+00)    0.99
## 
## --------------------------------------------------------------
## LUAD
## --------------------------------------------------------------
##                     beta         HR (95% CI for HR) p.value
## CD4T.E_lr        -0.0394 0.961 (8.10e-01--1.14e+00)    0.65
## Monocyte.E_lr    -0.0196 0.981 (8.43e-01--1.14e+00)     0.8
## B.E_lr            -0.127 0.881 (7.45e-01--1.04e+00)    0.14
## NK.E_lr            0.024  1.02 (8.83e-01--1.19e+00)    0.75
## Neutrophil.E_lr -0.00758 0.992 (8.68e-01--1.13e+00)    0.91
## Treg.E_lr         -0.118 0.888 (7.55e-01--1.05e+00)    0.16
## CD4T_lr          0.00119     1 (9.45e-01--1.06e+00)    0.97
## Monocyte_lr       0.0219  1.02 (9.29e-01--1.12e+00)    0.65
## B_lr             -0.0152 0.985 (8.74e-01--1.11e+00)     0.8
## NK_lr             0.0625  1.06 (9.78e-01--1.16e+00)    0.15
## Neutrophil_lr     0.0184  1.02 (9.45e-01--1.10e+00)    0.63
## Treg_lr           0.0114  1.01 (9.58e-01--1.07e+00)    0.68
## 
## --------------------------------------------------------------
## LUSC
## --------------------------------------------------------------
##                     beta         HR (95% CI for HR) p.value
## CD4T.E_lr         -0.054 0.947 (7.76e-01--1.16e+00)     0.6
## Monocyte.E_lr    -0.0136 0.986 (8.26e-01--1.18e+00)    0.88
## B.E_lr           -0.0392 0.962 (8.19e-01--1.13e+00)    0.63
## NK.E_lr            -0.04 0.961 (8.12e-01--1.14e+00)    0.64
## Neutrophil.E_lr   0.0621  1.06 (9.15e-01--1.24e+00)    0.42
## Treg.E_lr        -0.0143 0.986 (8.14e-01--1.19e+00)    0.88
## CD4T_lr           0.0229  1.02 (9.46e-01--1.11e+00)    0.57
## Monocyte_lr       0.0292  1.03 (9.17e-01--1.16e+00)    0.62
## B_lr              -0.138 0.871 (7.45e-01--1.02e+00)   0.085
## NK_lr           -0.00197 0.998 (9.01e-01--1.11e+00)    0.97
## Neutrophil_lr   -0.00117 0.999 (9.19e-01--1.09e+00)    0.98
## Treg_lr           0.0251  1.03 (9.57e-01--1.10e+00)    0.48
## 
## --------------------------------------------------------------
## SKCM
## --------------------------------------------------------------
##                   beta        HR (95% CI for HR) p.value
## CD4T.E_lr       0.0775 1.08 (9.79e-01--1.19e+00)    0.12
## Monocyte.E_lr    0.145 1.16 (1.06e+00--1.27e+00)  0.0019
## B.E_lr          0.0742 1.08 (9.84e-01--1.18e+00)    0.11
## NK.E_lr          0.128 1.14 (1.03e+00--1.26e+00)   0.014
## Neutrophil.E_lr  0.126 1.13 (1.05e+00--1.22e+00)   0.001
## Treg.E_lr        0.157 1.17 (1.04e+00--1.31e+00)  0.0087
## CD4T_lr         0.0916  1.1 (1.03e+00--1.16e+00)  0.0023
## Monocyte_lr      0.117 1.12 (1.05e+00--1.20e+00) 0.00089
## B_lr            0.0575 1.06 (9.80e-01--1.14e+00)    0.14
## NK_lr           0.0761 1.08 (1.02e+00--1.14e+00)   0.011
## Neutrophil_lr    0.094  1.1 (1.05e+00--1.15e+00) 0.00011
## Treg_lr         0.0919  1.1 (1.05e+00--1.15e+00)   1e-04

Generate plots of survival curves with respect to cell type fractions for SKCM.

Generate plots of survival curves with respect to relative cell type fractions for SKCM.

3 Assess the associations between mutation load and cell type fractions

First load mutation burden data

## $COAD
## [1] 185  49
## 
## $LUAD
## [1] 386  49
## 
## $LUSC
## [1] 296  49
## 
## $SKCM
## [1] 391  49
## $COAD
## [1] 177  76
## 
## $LUAD
## [1] 349  76
## 
## $LUSC
## [1] 274  76
## 
## $SKCM
## [1] 357  76

Next assess the associations between mutation load and cell type fractions

## 
## --------------------------------------------------------------
## COAD
## --------------------------------------------------------------
##                 mb1    mb2 mb1.pval mb2.pval
## CD4T.E       -0.133 -0.178   0.0790    0.018
## CD8T.E        0.171  0.131   0.0230    0.081
## Monocyte.E    0.065  0.014   0.3900    0.850
## B.E          -0.041 -0.104   0.5900    0.170
## NK.E          0.123  0.094   0.1000    0.210
## Neutrophil.E  0.048  0.049   0.5200    0.510
## Treg.E        0.100  0.011   0.1800    0.880
## CD4T         -0.130 -0.162   0.0840    0.031
## CD8T          0.237  0.210   0.0015    0.005
## Monocyte     -0.002 -0.073   0.9800    0.330
## B             0.024 -0.042   0.7500    0.580
## NK            0.013 -0.009   0.8600    0.910
## Neutrophil    0.002 -0.004   0.9800    0.960
## Treg         -0.152 -0.154   0.0430    0.041

## 
## --------------------------------------------------------------
## LUAD
## --------------------------------------------------------------
##                 mb1    mb2 mb1.pval mb2.pval
## CD4T.E       -0.061 -0.057  2.6e-01  3.0e-01
## CD8T.E        0.139  0.117  9.6e-03  3.1e-02
## Monocyte.E   -0.141 -0.113  8.5e-03  3.8e-02
## B.E          -0.010 -0.029  8.6e-01  5.9e-01
## NK.E          0.085  0.076  1.1e-01  1.7e-01
## Neutrophil.E  0.005 -0.017  9.3e-01  7.5e-01
## Treg.E       -0.062 -0.051  2.5e-01  3.5e-01
## CD4T         -0.340 -0.276  7.0e-11  2.6e-07
## CD8T          0.151  0.132  4.9e-03  1.5e-02
## Monocyte     -0.009  0.016  8.7e-01  7.8e-01
## B             0.010 -0.003  8.6e-01  9.6e-01
## NK            0.067  0.069  2.1e-01  2.1e-01
## Neutrophil   -0.103 -0.119  5.5e-02  2.8e-02
## Treg         -0.159 -0.163  3.0e-03  2.7e-03

## 
## --------------------------------------------------------------
## LUSC
## --------------------------------------------------------------
##                 mb1    mb2 mb1.pval mb2.pval
## CD4T.E       -0.211 -0.237  4.6e-04  8.2e-05
## CD8T.E       -0.019 -0.094  7.6e-01  1.2e-01
## Monocyte.E   -0.256 -0.244  1.9e-05  5.1e-05
## B.E          -0.171 -0.200  4.7e-03  9.3e-04
## NK.E         -0.072 -0.093  2.4e-01  1.3e-01
## Neutrophil.E  0.018  0.046  7.7e-01  4.5e-01
## Treg.E        0.014 -0.058  8.1e-01  3.4e-01
## CD4T          0.107  0.130  7.8e-02  3.2e-02
## CD8T         -0.181 -0.271  2.7e-03  5.9e-06
## Monocyte     -0.132 -0.113  2.9e-02  6.2e-02
## B            -0.193 -0.249  1.4e-03  3.4e-05
## NK           -0.089 -0.080  1.4e-01  1.9e-01
## Neutrophil   -0.103 -0.083  9.0e-02  1.7e-01
## Treg          0.180  0.214  2.8e-03  3.9e-04

## 
## --------------------------------------------------------------
## SKCM
## --------------------------------------------------------------
##                 mb1    mb2 mb1.pval mb2.pval
## CD4T.E        0.064  0.028    0.230    0.600
## CD8T.E        0.102  0.045    0.056    0.400
## Monocyte.E   -0.031 -0.042    0.560    0.440
## B.E           0.042 -0.013    0.440    0.810
## NK.E          0.026  0.036    0.620    0.510
## Neutrophil.E  0.016  0.034    0.760    0.530
## Treg.E        0.050  0.008    0.350    0.890
## CD4T         -0.069 -0.076    0.190    0.160
## CD8T          0.132  0.078    0.013    0.150
## Monocyte      0.012  0.023    0.820    0.670
## B             0.051  0.010    0.340    0.850
## NK            0.104  0.124    0.051    0.021
## Neutrophil   -0.055  0.004    0.300    0.940
## Treg         -0.101 -0.101    0.058    0.061

Illustrate cell type fraction estimates

## $COAD
## [1] 177  76
## 
## $LUAD
## [1] 349  76
## 
## $LUSC
## [1] 274  76
## 
## $SKCM
## [1] 357  76
## [1] 1157   76
##   bcr_patient_barcode SMASH_S_hg38 SMASH_oE_hg38 SMASH_wE_hg38 SMASH_oNE_hg38
## 1        TCGA-A6-2671            3          1.06     0.9274599      0.5531430
## 2        TCGA-A6-2675            2          0.68     0.7213201      0.6600493
##   SMASH_wNE_hg38 AscatPurity AscatPloidy raw_MB_hg38_SNV raw_MB_hg38_INDEL
## 1      0.4846527        0.68    3.609337              49                 7
## 2      0.6585205        0.49    3.351309              72                 2
##   IDH_CNV_status_hg38 tCN_burden tCN_burden_ap tumor_type.x num_clonal
## 1       IDH wild type   2.228662     1.0712969         COAD         39
## 2       IDH wild type   1.572784     0.8041944         COAD         46
##   num_subclonal prop_clonal gender.x age tumor_type.y
## 1            10   0.7959184     MALE  85        Colon
## 2            26   0.6388889     MALE  78        Colon
##   initial_pathologic_diagnosis_method  histological_type.x
## 1                                <NA> Colon Adenocarcinoma
## 2                                <NA> Colon Adenocarcinoma
##   yr_of_tobacco_smoking_onset pathologic_T stage    Time Delta
## 1                        <NA>           T3    IV 1331.01     1
## 2                        <NA>           T3    II 1321.01     0
##   radiation_therapy patient_id     CD4T.E     CD8T.E Monocyte.E        B.E
## 1                NO       2671 0.07669056 0.02889390 0.03723064 0.05887684
## 2                NO       2675 0.14310630 0.05848576 0.09817728 0.14408533
##         NK.E Neutrophil.E     Treg.E       CD4T       CD8T   Monocyte
## 1 0.01678819   0.02455244 0.02696743 0.04567977 0.00500000 0.06194856
## 2 0.03417972   0.04044031 0.06152530 0.17356475 0.09491321 0.07218969
##            B         NK Neutrophil       Treg ...1 type
## 1 0.02762686 0.00500000 0.05317235 0.08157246 1961 COAD
## 2 0.06759522 0.03352732 0.03273829 0.10547152 1964 COAD
##   age_at_initial_pathologic_diagnosis gender.y  race
## 1                                  85     MALE WHITE
## 2                                  78     MALE WHITE
##   ajcc_pathologic_tumor_stage   clinical_stage  histological_type.y
## 1                    Stage IV [Not Applicable] Colon Adenocarcinoma
## 2                   Stage IIA [Not Applicable] Colon Adenocarcinoma
##   histological_grade initial_pathologic_dx_year menopause_status birth_days_to
## 1    [Not Available]                       2009  [Not Available]        -31329
## 2    [Not Available]                       2009  [Not Available]        -28813
##   vital_status tumor_status last_contact_days_to death_days_to  cause_of_death
## 1         Dead   WITH TUMOR                   NA          1331 [Not Available]
## 2        Alive   TUMOR FREE                 1321            NA [Not Available]
##   new_tumor_event_type new_tumor_event_site new_tumor_event_site_other
## 1                 <NA>                 <NA>                       <NA>
## 2                 <NA>                 <NA>                       <NA>
##   new_tumor_event_dx_days_to treatment_outcome_first_course margin_status
## 1                        535                [Not Available]          <NA>
## 2                         NA    Complete Remission/Response          <NA>
##   residual_tumor OS OS.time DSS DSS.time DFI DFI.time PFI PFI.time Redaction
## 1             NA  1    1331   1     1331  NA       NA   1      535      <NA>
## 2             NA  0    1321   0     1321   0     1321   0     1321      <NA>
##  [1] "bcr_patient_barcode"                 "SMASH_S_hg38"                       
##  [3] "SMASH_oE_hg38"                       "SMASH_wE_hg38"                      
##  [5] "SMASH_oNE_hg38"                      "SMASH_wNE_hg38"                     
##  [7] "AscatPurity"                         "AscatPloidy"                        
##  [9] "raw_MB_hg38_SNV"                     "raw_MB_hg38_INDEL"                  
## [11] "IDH_CNV_status_hg38"                 "tCN_burden"                         
## [13] "tCN_burden_ap"                       "tumor_type.x"                       
## [15] "num_clonal"                          "num_subclonal"                      
## [17] "prop_clonal"                         "gender.x"                           
## [19] "age"                                 "tumor_type.y"                       
## [21] "initial_pathologic_diagnosis_method" "histological_type.x"                
## [23] "yr_of_tobacco_smoking_onset"         "pathologic_T"                       
## [25] "stage"                               "Time"                               
## [27] "Delta"                               "radiation_therapy"                  
## [29] "patient_id"                          "CD4T.E"                             
## [31] "CD8T.E"                              "Monocyte.E"                         
## [33] "B.E"                                 "NK.E"                               
## [35] "Neutrophil.E"                        "Treg.E"                             
## [37] "CD4T"                                "CD8T"                               
## [39] "Monocyte"                            "B"                                  
## [41] "NK"                                  "Neutrophil"                         
## [43] "Treg"                                "...1"                               
## [45] "type"                                "age_at_initial_pathologic_diagnosis"
## [47] "gender.y"                            "race"                               
## [49] "ajcc_pathologic_tumor_stage"         "clinical_stage"                     
## [51] "histological_type.y"                 "histological_grade"                 
## [53] "initial_pathologic_dx_year"          "menopause_status"                   
## [55] "birth_days_to"                       "vital_status"                       
## [57] "tumor_status"                        "last_contact_days_to"               
## [59] "death_days_to"                       "cause_of_death"                     
## [61] "new_tumor_event_type"                "new_tumor_event_site"               
## [63] "new_tumor_event_site_other"          "new_tumor_event_dx_days_to"         
## [65] "treatment_outcome_first_course"      "margin_status"                      
## [67] "residual_tumor"                      "OS"                                 
## [69] "OS.time"                             "DSS"                                
## [71] "DSS.time"                            "DFI"                                
## [73] "DFI.time"                            "PFI"                                
## [75] "PFI.time"                            "Redaction"

Compare cell type fraction estimates between gene expression and DNA methylation

Compare cell type fraction estimates vs. mutation load

5 Session information

## R version 3.6.2 (2019-12-12)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] tidyr_1.0.2          ggcorrplot_0.1.3     stargazer_5.2.2     
##  [4] readxl_1.3.1         survminer_0.4.8      survival_3.1-8      
##  [7] ggpointdensity_0.1.0 ggpubr_0.2.5         magrittr_1.5        
## [10] ggplot2_3.3.1        data.table_1.12.8   
## 
## loaded via a namespace (and not attached):
##  [1] zoo_1.8-7        tidyselect_1.0.0 xfun_0.12        reshape2_1.4.3  
##  [5] purrr_0.3.3      splines_3.6.2    lattice_0.20-38  colorspace_1.4-1
##  [9] vctrs_0.3.0      generics_0.0.2   htmltools_0.4.0  mgcv_1.8-31     
## [13] yaml_2.2.1       utf8_1.1.4       survMisc_0.5.5   rlang_0.4.6     
## [17] pillar_1.4.3     glue_1.3.1       withr_2.1.2      plyr_1.8.5      
## [21] lifecycle_0.2.0  stringr_1.4.0    munsell_0.5.0    ggsignif_0.6.0  
## [25] gtable_0.3.0     cellranger_1.1.0 evaluate_0.14    labeling_0.3    
## [29] knitr_1.28       fansi_0.4.1      broom_0.5.6      Rcpp_1.0.3      
## [33] xtable_1.8-4     scales_1.1.0     backports_1.1.5  farver_2.0.3    
## [37] km.ci_0.5-2      gridExtra_2.3    digest_0.6.23    stringi_1.4.5   
## [41] dplyr_0.8.4      KMsurv_0.1-5     cowplot_1.0.0    grid_3.6.2      
## [45] cli_2.0.1        tools_3.6.2      tibble_3.0.1     crayon_1.3.4    
## [49] pkgconfig_2.0.3  ellipsis_0.3.0   Matrix_1.2-18    assertthat_0.2.1
## [53] rmarkdown_2.1    R6_2.4.1         nlme_3.1-144     compiler_3.6.2